Prediction and assignment of function for a divergent N-succinyl amino acid racemase View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2007-08

AUTHORS

Ling Song, Chakrapani Kalyanaraman, Alexander A Fedorov, Elena V Fedorov, Margaret E Glasner, Shoshana Brown, Heidi J Imker, Patricia C Babbitt, Steven C Almo, Matthew P Jacobson, John A Gerlt

ABSTRACT

The protein databases contain many proteins with unknown function. A computational approach for predicting ligand specificity that requires only the sequence of the unknown protein would be valuable for directing experiment-based assignment of function. We focused on a family of unknown proteins in the mechanistically diverse enolase superfamily and used two approaches to assign function: (i) enzymatic assays using libraries of potential substrates, and (ii) in silico docking of the same libraries using a homology model based on the most similar (35% sequence identity) characterized protein. The results matched closely; an experimentally determined structure confirmed the predicted structure of the substrate-liganded complex. We assigned the N-succinyl arginine/lysine racemase function to the family, correcting the annotation (L-Ala-D/L-Glu epimerase) based on the function of the most similar characterized homolog. These studies establish that ligand docking to a homology model can facilitate functional assignment of unknown proteins by restricting the identities of the possible substrates that must be experimentally tested. More... »

PAGES

486

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nchembio.2007.11

DOI

http://dx.doi.org/10.1038/nchembio.2007.11

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1012134964

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/17603539


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Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

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curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nchembio.2007.11'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nchembio.2007.11'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nchembio.2007.11'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nchembio.2007.11'


 

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